Variant report

Variant	rs2144861
Chromosome Location	chr10:52309756-52309757
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52308145..52313390-chr10:52380498..52385309,7	K562	blood:
2	chr10:52305141..52307249-chr10:52308669..52310332,3	K562	blood:
3	chr10:52308481..52311283-chr10:52312051..52314747,2	MCF-7	breast:
4	chr10:52308954..52311040-chr10:52345342..52347602,2	K562	blood:
5	chr10:52309255..52311683-chr10:52321787..52323365,2	K562	blood:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000251950	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1010930	0.94[ASN][1000 genomes]
rs10763535	0.94[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10763550	0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs10763560	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10763566	0.82[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10826149	0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10826155	0.93[ASN][1000 genomes]
rs10826159	0.93[ASN][1000 genomes]
rs10826160	0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10826161	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10826163	0.94[ASN][1000 genomes]
rs10826164	0.94[ASN][1000 genomes]
rs10826165	0.94[ASN][1000 genomes]
rs10826166	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10826167	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10826169	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10826170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826228	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11005579	0.92[CEU][hapmap]
rs11006054	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11006075	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11006084	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11006114	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11006118	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11006141	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.94[ASN][1000 genomes]
rs11006160	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11006201	0.81[ASN][1000 genomes]
rs11006217	0.87[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.84[ASN][1000 genomes]
rs12219692	0.94[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12415817	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12415836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12572387	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1884570	0.94[ASN][1000 genomes]
rs2024872	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2224249	0.87[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs3011777	0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs34659292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36122110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4935173	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4935174	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935728	0.80[EUR][1000 genomes]
rs4935733	0.81[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7074764	0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7078284	0.82[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7088141	0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7094143	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7893884	0.81[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7900424	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7907260	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7915606	0.83[ASN][1000 genomes]
rs7916397	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.94[ASN][1000 genomes]
rs7920818	0.81[MEX][hapmap];0.86[TSI][hapmap]
rs7922802	0.86[TSI][hapmap]
rs9299582	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.94[ASN][1000 genomes]
rs9919413	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52299000-52310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:52299200-52310200	Weak transcription	Pancreas	Pancrea
4	chr10:52299600-52320600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:52300600-52310200	Weak transcription	Placenta	Placenta
6	chr10:52300800-52310800	Weak transcription	Gastric	stomach
7	chr10:52300800-52322800	Weak transcription	Primary B cells from cord blood	blood
8	chr10:52301600-52310200	Weak transcription	Left Ventricle	heart
9	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:52303200-52310200	Weak transcription	Fetal Lung	lung
11	chr10:52303200-52310200	Weak transcription	Stomach Mucosa	stomach
12	chr10:52303200-52312200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr10:52303400-52310200	Weak transcription	Spleen	Spleen
14	chr10:52303400-52310800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr10:52303400-52312200	Weak transcription	Adipose Nuclei	Adipose
16	chr10:52303400-52314000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr10:52304000-52312000	Weak transcription	Colon Smooth Muscle	Colon
18	chr10:52304400-52312000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:52305000-52309800	Weak transcription	Brain Anterior Caudate	brain
20	chr10:52305000-52310000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr10:52305000-52310200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr10:52305000-52310200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr10:52305200-52309800	Weak transcription	Brain Angular Gyrus	brain
24	chr10:52305200-52310000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr10:52305200-52310000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:52305200-52310200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr10:52305200-52310200	Weak transcription	Right Ventricle	heart
28	chr10:52305400-52329600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr10:52305800-52310400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:52306000-52310000	Weak transcription	Psoas Muscle	Psoas
31	chr10:52306000-52312600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr10:52306000-52312800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr10:52306000-52312800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr10:52306000-52314200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr10:52306000-52316000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr10:52306000-52319000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:52306000-52321400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr10:52306000-52322000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr10:52306000-52331800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr10:52306200-52310000	Weak transcription	HepG2	liver
41	chr10:52308000-52337200	Weak transcription	Primary T cells from cord blood	blood
42	chr10:52308800-52309800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:52308800-52312000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:52309200-52309800	Enhancers	Fetal Heart	heart
45	chr10:52309200-52310400	Enhancers	Lung	lung
46	chr10:52309200-52312600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr10:52309400-52309800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:52309400-52309800	Weak transcription	Fetal Intestine Large	intestine
49	chr10:52309400-52309800	Weak transcription	Ovary	ovary
50	chr10:52309400-52309800	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links